why not develop a template as one file and than break it apart into the different section. header, main, footer, sidebar.
i think you can do it as single file but that mean you will have to do the samething for archives, pages, etc. since this pages call the individuals header, footer and siderbar. sometimes the best thing to do is to take someone theme and user the php structure and than develop your css for it. this is what i did with mine blog, http://www.fusionrain.com/blog i still tweaking since i have some issues with the browsers.